5D57

In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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Literature

In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.

Huang, C.Y., Olieric, V., Ma, P., Howe, N., Vogeley, L., Liu, X., Warshamanage, R., Weinert, T., Panepucci, E., Kobilka, B., Diederichs, K., Wang, M., Caffrey, M.

(2016) Acta Crystallogr D Struct Biol 72: 93-112

  • DOI: https://doi.org/10.1107/S2059798315021683
  • Primary Citation of Related Structures:  
    5D52, 5D53, 5D54, 5D56, 5D57, 5D58, 5D59, 5D5A, 5D5B, 5D5C, 5D5D, 5D5E, 5D5F

  • PubMed Abstract: 

    • Here, a method for presenting crystals of soluble and membrane proteins growing in the lipid cubic or sponge phase for in situ diffraction data collection at cryogenic temperatures is introduced. The method dispenses with the need for the technically demanding and inefficient crystal-harvesting step that is an integral part of the lipid cubic phase or in meso method of growing crystals ...

    Here, a method for presenting crystals of soluble and membrane proteins growing in the lipid cubic or sponge phase for in situ diffraction data collection at cryogenic temperatures is introduced. The method dispenses with the need for the technically demanding and inefficient crystal-harvesting step that is an integral part of the lipid cubic phase or in meso method of growing crystals. Crystals are dispersed in a bolus of mesophase sandwiched between thin plastic windows. The bolus contains tens to hundreds of crystals, visible with an in-line microscope at macromolecular crystallography synchrotron beamlines and suitably disposed for conventional or serial crystallographic data collection. Wells containing the crystal-laden boluses are removed individually from hermetically sealed glass plates in which crystallization occurs, affixed to pins on goniometer bases and excess precipitant is removed from around the mesophase. The wells are snap-cooled in liquid nitrogen, stored and shipped in Dewars, and manually or robotically mounted on a goniometer in a cryostream for diffraction data collection at 100 K, as is performed routinely with standard, loop-harvested crystals. The method is a variant on the recently introduced in meso in situ serial crystallography (IMISX) method that enables crystallographic measurements at cryogenic temperatures where crystal lifetimes are enormously enhanced whilst reducing protein consumption dramatically. The new approach has been used to generate high-resolution crystal structures of a G-protein-coupled receptor, α-helical and β-barrel transporters and an enzyme as model integral membrane proteins. Insulin and lysozyme were used as test soluble proteins. The quality of the data that can be generated by this method was attested to by performing sulfur and bromine SAD phasing with two of the test proteins.

    Organizational Affiliation: 

    Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Diacylglycerol kinase
A, B, C, D, E, F
A, B, C, D, E, F
130Escherichia coli K-12Mutation(s): 7 
Gene Names: dgkA, b4042, JW4002, dgk
EC: 2.7.1.107
Membrane Entity: Yes 
UniProt
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Explore P0ABN1 
Go to UniProtKB:  P0ABN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABN1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.32α = 90
b = 91.34β = 90
c = 143.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1255

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references